GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Desulfovibrio vulgaris Miyazaki F

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 8501405 DvMF_2135 TRAP dicarboxylate transporter, DctP subunit (RefSeq)

Query= SwissProt::P37735
         (333 letters)



>FitnessBrowser__Miya:8501405
          Length = 365

 Score =  143 bits (360), Expect = 8e-39
 Identities = 93/290 (32%), Positives = 152/290 (52%), Gaps = 7/290 (2%)

Query: 5   RILGALVGATALSLALSVPA----LAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNG 60
           R L A +G     LA  +P      +    +  + V  P + +   A +F +L E+ ++G
Sbjct: 31  RALAASLGLMLACLAAILPGWPRTASAATELTLAVVTTPGSAQHVCAERFRQLLEERSHG 90

Query: 61  AVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEAL 120
           A  V V+ +  L  + E L+ LQLG VQ+   +L    P  V + +V D P++F+D    
Sbjct: 91  AYRVVVHHSGTLGTETEILQQLQLGGVQLAIITLGVLDPF-VPEVKVLDYPFLFRDAAEA 149

Query: 121 HKVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANT-PLTMPDDFLGLKMRIQSSKVL 179
            +V  G  G+ LL  LE  G+ GL F +NGF+ ++ N  P+   DD  GLK+R+  S + 
Sbjct: 150 DRVLDGATGRALLDALERVGLKGLHFSENGFRHLTNNVRPVRSVDDVRGLKIRVLESTLH 209

Query: 180 EAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGY 239
                ALGA P  M +  +Y  LQ G +DG ENP   M   +M EVQK+ +++ H Y  +
Sbjct: 210 RELWRALGANPTPMGWP-IYAELQQGTIDGQENPLWVMAEYRMPEVQKYLSLTGHVYSAH 268

Query: 240 AVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAG 289
           A + N  +++GLP   RT + + MA++  Y     ++++   L+ +++AG
Sbjct: 269 ADLANLAWFNGLPPAERTLVMQCMADAAAYQRAYNRQKDADYLRRLREAG 318


Lambda     K      H
   0.314    0.130    0.364 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 211
Number of extensions: 7
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 333
Length of database: 365
Length adjustment: 29
Effective length of query: 304
Effective length of database: 336
Effective search space:   102144
Effective search space used:   102144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory